@awnlee jawkingI recall a story that may be the one you referenced. It came out about the same time as The Man in the High Castle by Philip K. Dick (1962 for Dick's story). I have read there's no connection between the two stories, though I don't know if that's true.
In the story, a Los Alamos scientist has doubts about the morality of using the A-bomb on Japan. He is transported to an alternate future where Japan has rallied and conquered America. In the end, he realizes it's necessary that America use nuclear weapons to defeat Japan. He is transported back to 1945 Los Alamos so he can continue working on the A-bomb.
Unfortunately, I don't remember the title or author, but a search of stories similar to The Man in the High Castle might turn it up.